Merge pull request #35 from JuliaGraphs/cleanup

cleanup

Author: bramtayl

.JuliaFormatter.toml

@@ -0,0 +1,6 @@
+always_for_in = true
+whitespace_typedefs = true
+whitespace_ops_in_indices = true
+remove_extra_newlines = true
+import_to_using = true
+short_to_long_function_def = true

.github/workflows/test.yml

@@ -9,7 +9,7 @@ jobs:
     strategy:
       matrix:
         version:
-          - '1.0'
+          - '1.6'
           - '1'
           - 'nightly'
     steps:

Project.toml

@@ -9,7 +9,7 @@ JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 [compat]
 Graphs = "1.4.1"
 JLD2 = "0.1.11, 0.2, 0.3, 0.4"
-julia = "1"
+julia = "1.6"
 
 [extras]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"

docs/make.jl

@@ -18,7 +18,7 @@ makedocs(
             "Reading / writing" => "tutorial_files.md",
         ],
         "API reference" => "api.md",
-    ]
+    ],
 )
 
 deploydocs(repo = "github.com/JuliaGraphs/MetaGraphsNext.jl.git")

docs/src/tutorial_basics.md

@@ -12,7 +12,7 @@ We provide a default constructor in which you only need to specify types:
 
 ```jldoctest example
 julia> colors = MetaGraph( Graph(), VertexData = String, EdgeData = Symbol, graph_data = "graph_of_colors")
-Meta graph based on a {0, 0} undirected simple Int64 graph with vertex labels of type Symbol, vertex metadata of type String, edge metadata of type Symbol, graph metadata given by "graph_of_colors", and default weight 1.0
+Meta graph based on a Graphs.SimpleGraphs.SimpleGraph{Int64}(0, Vector{Int64}[]) with vertex labels of type Symbol, vertex metadata of type String, edge metadata of type Symbol, graph metadata given by "graph_of_colors", and default weight 1.0
 ```
 
 ## Modifying the graph
@@ -136,7 +136,7 @@ julia> size(weight_matrix)
 julia> weight_matrix[1, 3]
 1.0
 
-julia> weight_function(weighted)(0)
+julia> get_weight_function(weighted)(0)
 0
 ```
 

src/MetaGraphsNext.jl

@@ -5,7 +5,7 @@ using Graphs
 
 export MetaGraph, MetaDiGraph, MetaUndirectedGraph
 export label_for, code_for, set_data
-export weighttype, default_weight, weight_function
+export weighttype, default_weight, get_weight_function
 export MGFormat, DOTFormat
 
 include("metagraph.jl")

src/dict_utils.jl

@@ -1,120 +1,123 @@
 """
-    getindex(g)
+    getindex(meta_graph)
 
-Return graph metadata.
+Return meta_graph metadata.
 """
-Base.getindex(g::MetaGraph) = g.graph_data
+function Base.getindex(meta_graph::MetaGraph)
+    meta_graph.graph_data
+end
 
 """
-    getindex(g, label)
+    getindex(meta_graph, label)
 
 Return vertex metadata for `label`.
 """
-Base.getindex(g::MetaGraph, label) = g.vertex_properties[label][2]
+function Base.getindex(meta_graph::MetaGraph, label)
+    meta_graph.vertex_properties[label][2]
+end
 
 """
-    getindex(g, label_1, label_2)
+    getindex(meta_graph, label_1, label_2)
 
 Return edge metadata for the edge between `label_1` and `label_2`.
 """
-Base.getindex(g::MetaGraph, label_1, label_2) = g.edge_data[arrange(g, label_1, label_2)]
+function Base.getindex(meta_graph::MetaGraph, label_1, label_2)
+    meta_graph.edge_data[arrange(meta_graph, label_1, label_2)]
+end
 
 """
-    haskey(g, label)
+    haskey(meta_graph, label)
 
-Determine whether a graph `g` contains the vertex `label`.
+Determine whether a meta_graph `meta_graph` contains the vertex `label`.
 """
-Base.haskey(g::MetaGraph, label) = haskey(g.vertex_properties, label)
+function Base.haskey(meta_graph::MetaGraph, label)
+    haskey(meta_graph.vertex_properties, label)
+end
 
 """
-    haskey(g, label_1, label_2)
+    haskey(meta_graph, label_1, label_2)
 
-Determine whether a graph `g` contains an edge from `label_1` to `label_2`.
+Determine whether a meta_graph `meta_graph` contains an edge from `label_1` to `label_2`.
 
-The order of `label_1` and `label_2` only matters if `g` is a digraph.
+The order of `label_1` and `label_2` only matters if `meta_graph` is a digraph.
 """
-function Base.haskey(g::MetaGraph, label_1, label_2)
-    return (
-        haskey(g, label_1) &&
-        haskey(g, label_2) &&
-        haskey(g.edge_data, arrange(g, label_1, label_2))
-    )
+function Base.haskey(meta_graph::MetaGraph, label_1, label_2)
+    haskey(meta_graph, label_1) &&
+    haskey(meta_graph, label_2) &&
+    haskey(meta_graph.edge_data, arrange(meta_graph, label_1, label_2))
 end
 
 """
-    setindex!(g, data, label)
+    setindex!(meta_graph, data, label)
 
 Set vertex metadata for `label` to `data`.
 """
-function Base.setindex!(g::MetaGraph, data, label)
-    if haskey(g, label)
-        set_data!(g, label, data)
+function Base.setindex!(meta_graph::MetaGraph, data, label)
+    if haskey(meta_graph, label)
+        set_data!(meta_graph, label, data)
     else
-        add_vertex!(g, label, data)
+        add_vertex!(meta_graph, label, data)
     end
-    return nothing
+    nothing
 end
 
 """
-    setindex!(g, data, label_1, label_2)
+    setindex!(meta_graph, data, label_1, label_2)
 
 Set edge metadata for `(label_1, label_2)` to `data`.
 """
-function Base.setindex!(g::MetaGraph, data, label_1, label_2)
-    if haskey(g, label_1, label_2)
-        set_data!(g, label_1, label_2, data)
+function Base.setindex!(meta_graph::MetaGraph, data, label_1, label_2)
+    if haskey(meta_graph, label_1, label_2)
+        set_data!(meta_graph, label_1, label_2, data)
     else
-        add_edge!(g, label_1, label_2, data)
+        add_edge!(meta_graph, label_1, label_2, data)
     end
-    return nothing
+    nothing
 end
 
 """
-    delete!(g, label)
+    delete!(meta_graph, label)
 
 Delete vertex `label`.
 """
-function Base.delete!(g::MetaGraph, label)
-    if haskey(g, label)
-        v = code_for(g, label)
-        _rem_vertex!(g, label, v)
+function Base.delete!(meta_graph::MetaGraph, label)
+    if haskey(meta_graph, label)
+        _rem_vertex!(meta_graph, label, code_for(meta_graph, label))
     end
-    return nothing
+    nothing
 end
 
 """
-    delete!(g, label_1, label_2)
+    delete!(meta_graph, label_1, label_2)
 
 Delete edge `(label_1, label_2)`.
 """
-function Base.delete!(g::MetaGraph, label_1, label_2)
-    v1, v2 = code_for(g, label_1), code_for(g, label_2)
-    rem_edge!(g, v1, v2)
-    return nothing
+function Base.delete!(meta_graph::MetaGraph, label_1, label_2)
+    rem_edge!(meta_graph, code_for(meta_graph, label_1), code_for(meta_graph, label_2))
+    nothing
 end
 
 """
-    _copy_props!(oldg, newg, vmap)
+    _copy_props!(old_meta_graph, new_meta_graph, code_map)
 
-Copy properties from `oldg` to `newg` following vertex map `vmap`.
+Copy properties from `old_meta_graph` to `new_meta_graph` following vertex map `code_map`.
 """
-function _copy_props!(oldg::G, newg::G, vmap) where {G<:MetaGraph}
-    for (newv, oldv) in enumerate(vmap)
-        oldl = oldg.vertex_labels[oldv]
-        _, data = oldg.vertex_properties[oldl]
-        newg.vertex_labels[newv] = oldl
-        newg.vertex_properties[oldl] = (newv, data)
+function _copy_props!(old_meta_graph::MetaGraph, new_meta_graph::MetaGraph, code_map)
+    for (new_code, old_code) in enumerate(code_map)
+        old_label = old_meta_graph.vertex_labels[old_code]
+        _, data = old_meta_graph.vertex_properties[old_label]
+        new_meta_graph.vertex_labels[new_code] = old_label
+        new_meta_graph.vertex_properties[old_label] = (new_code, data)
     end
-    for newe in edges(newg.graph)
-        vertex_labels = newg.vertex_labels
-        v1, v2 = Tuple(newe)
-        label_1 = vertex_labels[v1]
-        label_2 = vertex_labels[v2]
-        newg.edge_data[arrange(newg, label_1, label_2, v1, v2)] = oldg.edge_data[arrange(
-            oldg, label_1, label_2
-        )]
+    for new_edge in edges(new_meta_graph.graph)
+        vertex_labels = new_meta_graph.vertex_labels
+        code_1, code_2 = Tuple(new_edge)
+        label_1 = vertex_labels[code_1]
+        label_2 = vertex_labels[code_2]
+        new_meta_graph.edge_data[arrange(new_meta_graph, label_1, label_2, code_1, code_2)] =
+            old_meta_graph.edge_data[arrange(old_meta_graph, label_1, label_2)]
     end
-    return nothing
+    nothing
 end
 
 # TODO - It would be nice to be able to apply a function to properties.